I reckon she just looks better and more like a scientist in her Chariots of the Dogs get-up than how she looked in the final episode of season two. Plus you need to remember she'd only just died in the latter and personal appearance can't have been a high priority on her agenda. To top all that, she appears in each episode how we'd pretty much expect/want to see her.
Telltale know what they're doing.
P.S. The hair's gone from her legs as well. The only part of her still ugly as f***.